Add minimap2 as aligner option for Bismark #455
Description
Description of feature
As requested by @sateeshperi, it would be nice to support minimap2 as alternative aligner for Bismark. Here are the options that are currently supported:
MINIMAP2-SPECIFIC OPTIONS:
--minimap2/--mm2
Uses minimap2 as the underlying read aligner. This mode is very new and currently experimental. The default mapping mode is --nanopore (preset -x map-ont (Nanopore reads)). Currently, there are no plans to support PacBio reads. Internally, minimap2 is run with the options -a --MD. More information here: https://lh3.github.io/minimap2/minimap2.html. Default: OFF.
--mm2_nanopore
Using the minimap2 preset for Oxford Nanopore (ONT) vs reference mapping (-x map-ont). Only works in conjunction with --minimap2. Default mode when --minimap2 is specified without additional qualifiers.
--mm2_pacbio
Using the minimap2 preset for PacBio vs reference mapping (-x map-pb). Only works in conjuntion with --minimap2. Default: OFF.
--mm2_short_reads
This option invokes the minmap2 preset setting -x sr and is intended for genomic short-read mapping with accurate reads (probably Illumina 150bp+ ?). For spliced short-reads, please use --hisat2 instead. The sr preset mode (short single-end reads without splicing) uses the following options: -k21 -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no. Default: OFF.
--mm2_maximum_length <int>
Maximum length cutoff for very long sequences (currently allowed 100-100,000 bp). Default: 10000.